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OTclust

R package OTclust

Providing mean partition for ensemble clustering by optimal transport alignment(OTA), uncertainty measures for both partition-wise and cluster-wise assessment and multiple visualization functions to show uncertainty, for instance, membership heat map and plot of covering point set. A partition refers to an overall clustering result.

To install this package, please run:

library(devtools)

install_github("LixiangZhang/OTclust")

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Version

Install

install.packages('OTclust')

Monthly Downloads

252

Version

1.0.6

License

GPL (>= 2)

Maintainer

Lixiang Zhang

Last Published

October 6th, 2023

Functions in OTclust (1.0.6)

sim1

Simulated toy data
mplot

Membership Heat Map
jaccard

Jaccard similarity matrix.
ensemble

Generate an ensemble of partitions.
cplot

Covering Point Set Plot
YAN

Single cell gene data from Yan's paper
otplot

Visualize a partition on 2 dimensional space
otclust

Mean partition by optimal transport alignment.
CPS

CPS Analysis on a collection of clustering results
clustCPS

CPS Analysis for cluster validation..
align

Optimal Transport Alignment
preprocess

Data preprocessing
wassDist

Wasserstein distance between two partitions.
perturb

Perturb data by adding noise, bootstrapping or mix-up
pplot

Point-wise Uncertainty Assessment
vis_pollen

Single cell gene visualization data from Pollen's paper
visCPS

CPS Analysis on selecting visualization method.